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Yorodumi- PDB-5wyq: Crystal Structure and catalytic mechanism of the essential m1G37 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wyq | ||||||
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Title | Crystal Structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa | ||||||
Components | tRNA (guanine-N(1)-)-methyltransferase | ||||||
Keywords | TRANSFERASE / Pseudomonas aeruginosa PA14 / tRNA (m1G37) methyltransferase / TrmD / tDNA modification | ||||||
Function / homology | Function and homology information tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Jaroensuk, J. / Liew, C.W. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Zhong, W. / McBee, M.E. / Maenpuen, S. / Prestwich, E.G. / DeMott, M.S. ...Jaroensuk, J. / Liew, C.W. / Atichartpongkul, S. / Chionh, Y.H. / Wong, Y.H. / Zhong, W. / McBee, M.E. / Maenpuen, S. / Prestwich, E.G. / DeMott, M.S. / Mongkolsuk, S. / Dedon, P.C. / Lescar, J. / Fuangthong, M. / Chaiyen, P. | ||||||
Citation | Journal: Rna / Year: 2019 Title: Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD fromPseudomonas aeruginosa. Authors: Jaroensuk, J. / Wong, Y.H. / Zhong, W. / Liew, C.W. / Maenpuen, S. / Sahili, A.E. / Atichartpongkul, S. / Chionh, Y.H. / Nah, Q. / Thongdee, N. / McBee, M.E. / Prestwich, E.G. / DeMott, M.S. ...Authors: Jaroensuk, J. / Wong, Y.H. / Zhong, W. / Liew, C.W. / Maenpuen, S. / Sahili, A.E. / Atichartpongkul, S. / Chionh, Y.H. / Nah, Q. / Thongdee, N. / McBee, M.E. / Prestwich, E.G. / DeMott, M.S. / Chaiyen, P. / Mongkolsuk, S. / Dedon, P. / Lescar, J. / Fuangthong, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wyq.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wyq.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wyq_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5wyq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5wyq_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 5wyq_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/5wyq ftp://data.pdbj.org/pub/pdb/validation_reports/wy/5wyq | HTTPS FTP |
-Related structure data
Related structure data | 5wyrC 6jkiC 1p9pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27864.502 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) Strain: UCBPP-PA14 / Gene: trmD, PA14_15990 / Plasmid: pNIC-CH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q02RL6, tRNA (guanine37-N1)-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.35 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris-Cl pH 8.4, 12% MPD, 12% PEG 1000, 12% PEG 3350, 5% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 18, 2015 / Details: Toroidal focusing |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→28.12 Å / Num. obs: 34505 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 51.63 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.16→2.29 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2943 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P9P Resolution: 2.16→28.12 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.214 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.184
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Displacement parameters | Biso mean: 59.88 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.16→28.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.16→2.23 Å / Total num. of bins used: 17
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